StarGate Atlantis: The Middle
by Atlantis410
Summary: Imagine yourself as a stick. There are two choices in the harsh environment: Fight off your preys and predators and turn into a violent, lethal weapon, or stay and try to stay strong throughout the whole time, but still stay the object you where suppose to be..a stick. -Atlantis410, Elizabeth Weir/John Sheppard pairing
1. Chapter 1: Pilot

Disclaimer: StarGate Atlantis doesn't belong to me!

Setting: Set in season 2

Pairing: Elizabeth Weir/ John Sheppard

* * *

 **Pilot**

 _Elizabeth_ ran into the gate room with a bullet-proof vest and a gun in her pocket.

"Umm...care to fill me in?"John said, confused by her appearance.

"I'm going with you guys to the planet." Elizabeth said, rolling her eyes.

"Their leader might be able to agree to an alliance and-"she continued.

"Okay! WE get the point!" Rodney cut her off, getting real impatient.

* _ **FlashBack**_ *

The gate turned on at an unexpected moment, bringing the water-like energy to explode out of the circle. Luckily, Elizabeth was in the room already. No IDC was received, but a radio signal came out of nowhere.

"Hello?"a voice came through. Nobody recognized the person. Elizabeth spoke,"Hello...who is this."

After a few seconds of waiting, the voice replied," I'm Katsha, leader of the people called the Dhunar. We need allies because of our enemies, the Wraith." The last word didn't shock them at all, since they have met a bunch of people who are against the Wraith.

"Uh..okay, let me and my people talk about this, and if we're okay, we can come over to your planet, right?" Elizabeth asked. "Sure!" Katsha said, before the Stargate turned off.

* ** _End of FlashBack_** *

John, Rodney, Teyla, Elizabeth, and Ronon stepped through the gate. It closed behind them as Ronon came through.

"Nnnniiiccccee!" exclaimed the lieutenant colonel when he saw the breathtaking view.

Every else also looked around in awe. "Let's go.."Ronon said, waving his hand over to the left.

There was a fountain in the middle of the area, and a bunch of blue and white buildings. There were statues and plants all over the place, along with people and children.

"Hello, again..."said Katsha.

 **TBC**

* * *

A/N: Thanks for reading! Sorry it was short. I'll try to make my next chapters longer.


	2. Chapter 2: Embarrassment

**Embarrassment**

"Hello, again..."said Katsha.

"Uhhh...hello Katsha." Teyla replied.

Katsha nodded, understanding that the team might be suspicious. "Here,"Katsha moved over, pointing her finger over to the field. "Follow me." The team- including Dr. Weir -followed her onto the grassy area.

As the team reached the meadow, Katsha paused for a second. Then she put her hand over a rock, and a door appeared out of nowhere.

"Amazing!" Rodney mumbled.

They stepped in and found themselves in a room. "Where are we?" Elizabeth asked.

"We are in one of our hidden rooms. The Wraith- for some reason - can't detect us while we're down here, so we're safe."a woman approached them.

"Who are you?" Ronon moved his gun up, so it pointed at the woman.

"She's one of my b-best scientists, Lekio." Katsha jumped in front of Lekio.

"Hello, it's very nice to meet you, Lekio" Teyla shook her hand after Katsha moved over.

After that, the whole team separated to explore. Ronon found and started to explore the weapon chamber. Rodney wanted to check out their power source, which was almost as powerful as a ZPM. Teyla was led by Lekio to a room filled with small, effective ships. That left Elizabeth and John alone in the main room.

"Do you trust Katsha and Lekio. I mean, they have proven trustworthy so far. But most of our enemies pretend to be a strong, helping civilization, and then they turn on us- like the Genii," John whispered to Elizabeth.

'Well, I'm not sure. I mean they're the best people who need allies we've come across so far..."Elizabeth said, biting her bottom lip.

"But...?"

"They could just be planning a scheme and doing things like this to throw us off track. They might try to destroy Atlantis, or..."

"Do you guys want to look around the place?" Lekio appeared out of nowhere, making them jump.

"No thanks." Elizabeth replied.

"There is also a room for married couples like you guys- who want to be alone," Lekio stated.

Elizabeth and John tensed up.

 _'Please don't tell me she said what I think she just said,'_ Elizabeth thought, covering her face. _' Don't blush..don't look at him...oh my lord.'_

"Uh..er...we're not married, we just work together. So, no thanks." John said, feeling embarrassed, too.

"Rrriiiggghhhttt. Okay, well, I'll be over there, so call out my name if you need me." Lekio pointed over to the empty hall.

 _'Oh..no,'_ John thought.

He looked at Elizabeth, who was still covering her face.

"Elizabeth?" he said, feeling really weird.

She just nodded, but slowly put her hands down, staring into the ground.

This was going to be an interesting, awkward time.

 **TBC**

* * *

A/N: Thanks for reading. So sorry if this was short was well.

 **I was so mad/sad when I wrote this chapter, I accidently push the back button when I almost finished the chp and I didn't save the doc, so I had to retyped the whole chapter. :D**


	3. Chapter 3 : Captured

**Captured**

"Are you okay, John and Elizabeth?" Teyla broke the silence. Elizabeth still had head down, so John answered," We're fine Teyla. Don't worry about us." Still confused, Teyla radioed Ronon and Mckay to come back to the main room.

When Ronon and Rodney finally made it to the room, Elizabeth noticed that the team was back and rose her head up.

Everyone ( Teyla, Rodney, and Ronon) stared at both of the leaders, wondering if they should continue and leave or wait for their responses. John was the first one to notice. "Uh..let's go try to find Katsha so we can get out of here." John suggested, since they couldn't seem to find the door they came through.

"Okay,"Ronon said, turning around.

They walked over to the empty hall, wondering if they could locate Lekio, first. She was nowhere to be seen.

"Okay then, Ronon, you go search the halls. Teyla, you could stay in the main room, just in case any of them- Katsha or Lekio -past by. Elizabeth, you could-"John commanded.

"I'll go with Teyla." Elizabeth cuts him.

"Okay then, I guess I'll go check the other spare room and Rodney, you could go with me," he said.

Everyone made their ways to their positions.

"Is there something wrong with you and Colonel Sheppard?" Teyla asked, feeling concerned.

"Oh no...nothing is wrong. We a-are..I-I mean t-th-there is..." Elizabeth stuttered.

"You don't have to tell me if you don't want to," Teyla said quickly, hoping she didn't upset Elizabeth.

Elizabeth just stayed silent.

* * *

"So, is there anything between you and Elizabeth. I mean, you guys were sort of acting weird when me and Ronon came back?"Rodney asked.

"No, it was nothing." he lied.

They already checked about 5 halls already, and they still couldn't find Lekio _and_ Katsha.

Rodney was about to say something else, when two armed men ran in front of them.

"What the-" John yelled, before his world flip over onto him and his face made contact with the floor.

* * *

Teyla and Elizabeth were walking, silently, around the room before they heard a shout.

 _'What on Earth?'_ Elizabeth thought.

They could only take one more step before Lekio walked through the halls.

"Grab them!" she said. "Both of them!"

Before they had time to react, they were both unconscious.

* * *

Rodney was the first to wake up. He looked around, noticing that everyone around him was unconscious and that he was in a huge jail cell. He tried to wake up John first.

"JOHN!"he screamed into his ear, jabbing him with his finger.

"Ooowwww..what the heck Mckay?"John groaned, holding his head.

Rodney turned around, but before he could try to wake up Ronon, John said." I think Ronon would kill you if you use the same strategy to wake me up on him."

"Ouccchhhh..." groaned a voice over in the corner. It was Elizabeth.

 _'I think I should help her. But what about that awkward situation earlier. I don't think she'll mind.'_ John thought.

He crawled over to the corner and gave out his hand.

Elizabeth opened her eyes to see he was trying to help her.

 _'What should I do? Should I take his hand? UUUUggghhhhh..come on, Elizabeth. You're going to have to move soon.'_ she thought.

Her hand was almost touching his, but then, she pulled back, hugging her hand like it was the only thing that could keep her alive.

John left his hand out a bit longer, but realizing she wasn't going to take it, he put it down. He was going to say something to her, but then there was a loud noise behind him, so he had to turn around.

"I see you guys have awaken," Katsha laughed." Now, who want's to be the first to _**die**_."

"Well, that's a bit too dramatic." John whispered.

Katsha look around the room, then pointed to someone. Everyone turned to see her victim.

"How about you..."

 **TBC**

* * *

A/N: Thanks for reading! I'm going to leave this at a cliffhanger. :3 Hope you enjoyed the story so far!


	4. Chapter 4: 2 Is Better than 1?

**2 is Better than 1?**

* * *

 _Previously_

 _"I see you guys have awaken," Katsha laughed." Now, who want's to be the first to **die**."_

 _"Well, that's a bit too dramatic." John whispered._

 _Katsha look around the room, then pointed to someone. Everyone turned to see her victim._

 _"How about you..."_

* * *

 _Now_

"How about you...John Sheppard."

Rodney gasped, looking at John, then back to Katsha. Teyla was surprised and was covering her mouth in shock. Ronon was staring angrily at Katsha, clutching his fist so hard that his knuckles were white. Elizabeth stood up.

"No..don't take him, take me. I'm the leader of the expedition..whatever you think he knows, I might know...but- please -don't kill him." Elizabeth said, begging the woman to let John live. Luckily, for Elizabeth, Katsha called Lekio, and they both started talking, but then that luck changed.

"Me and Lekio have come to a decision. We'll take both of you..but spare one. Unless Dr. Weir changes her mind..." Katsha glared at Elizabeth, then back to John.

Elizabeth was rethinking what to do and say next when John stood up as well.

"Elizabeth..don't do it. We could still protect Atlantis or whatever they want. Don't risk your own life to save mine," John whispered to Elizabeth, assuring her that it was okay.

It wasn't okay. They both knew that they couldn't live without each other..and they both knew that Elizabeth wouldn't let anyone _kill_ John..and John knew that she would risk her life for him.

"John, this is my choice." she said, quickly. They looked at each other in the eyes for a quick second- which felt like an eternity to them -then turned to Katsha and Lekio.

"Have you made your decision, yet? Lekio asked, crossing both her arms over her chest.

"Yes..I'm coming with John, but-" she said.

"Okay...now, let's go!" Katsha interrupted, while the guards approached Elizabeth and John, and grabbed them.

In a few seconds, they were both knocked out.

* * *

John woke up first, with a throbbing headache. _'What happened..where am I?'_ he thought. In a second, he had remembered what had happen. They were captured- by Lekio and Katsha -, Katsha chose him to die, and Elizabeth had risked her own life and went with him.

"'Lizabeth?" John called out. The room was either dark, or he was temporarily blind.

"J-John? Is that you?" another female voice asked. John could hear something moving towards him.

"Elizabeth? Are you okay?"

"Yes...I was probably awake- I think -about 2 hours ago...I couldn't find y-you...it's so dar-dark" Elizabeth's voice began to break.

"Oh...I'm sorry."

"It's okay, at least you're here, now."

They were always comfortable with each other, always told each other their opinions, thoughts, and secrets. But they only secret they hadn't told each other, was that they 'loved' each other.

The door- which was shaped like a small gate -opened and Katsha walked in.

"It seems that both of you have awaken," Katsha smirked. She walked forward, but left some distance between them just in case John and Elizabeth were going to attack her.

"Why are you doing this?" John frowned at her.

Katsha just ignored his question and continued.

"Here is your lunch. You will only get 3 servings each day. So, you might have to share your food. We want answers. Give us the locations of your worlds, you will be spared. Give us your mighty weapons- from your worlds-, you shall both earn full meals for each day. If you don't tell us anything or don't cooperate with us, we _will_ torture you until you _die_." Katsha finished, walking out of the door before Elizabeth or John could reply.

A guard came up to them, put a dish- covered with a piece of cloth -onto the floor, pressed a button- which turned on the lights, and locked the door. His footsteps disappeared in a few minutes.

On the dish was a few pieces of bread, small amount of chicken, and a medium-sized cup of water.

* * *

Ronon banged his hands onto the bar angrily.

"It's not going to work..." Rodney grumbled, telling Ronon for the 6th time.

"At least I'm doing something!" Ronon shouted back.

"Stop it," Teyla told them.

All three of them were still trapped, but mostly mad at their captors.

* * *

Elizabeth and John shared their meal. They both split the meal they got into halves. For the water, they did the same. After eating, Elizabeth and John both sat in the corner. The room was cold, so they just huddled up together, but tried keep their distance.

The light had started to flicker and other people voices were fading away.

"Do you think..that we are every going to get out of here?" Elizabeth asked, staring into his eyes. He smiled warmly.

"Hopefully," John said. Her head rested on his shoulder, tucked perfectly. His head was on top of hers.

The room was now silent, and the only sounds were their breaths. John scooted a bit closer to Elizabeth. She noticed, but was too tired to comment. She yawned and turned her body so that she was closer to him.

"Goodnight, John."

"Goodnight, 'Lizabeth."

 **TBC**

* * *

A/N: Thanks for reading. Haha..I'm starting not to really get my story! See ya! Twitter Account: PhoenixBurn45. _R & R_


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